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A Jedi ambush leaves the Sith ship Omen marooned on a remote alienworld, its survivors at the mercy of their desolate surroundings and facing almost certain death. But Sith will no more bow before the whims of fate than they will yield to the weapons of their enemies. And Omen's cunning commanderYaru Korsin will let nothing keep him and his crew from returning to the stars and rejoining the Sith order's conquest of the galaxy. Murdering his own brother has proven Korsin's ruthless resolve—but now an entire race stands in his way.

The primitive, superstitious Keshiri worship unseen gods called the Skyborn, shun science, and punish unbelievers with death. Branded a heretic the widowed young geologistAdari Vaal is running for her life. Among the mysterious Sith castaways she finds powerful sanctuary—and her saviors find the means of survival. With Adari as their willing pawn, the Skyborn as their Trojan horse, and the awesome power of the dark side of the Force at their command, the lost tribe of the Omen set out to subjugate a planet and its people—and lay the foundation for a merciless new Sith nation.

Skyborn is set in 5000 BBY and is told mainly from the point of view of Adari Vaal, a femaleKeshiri geologist and the widow of the late Zhari Vaal, a member of the Neshtovar. The Neshtovar were an elite aristocratic priesthood that rode uvaks, winged reptilian beasts of burden, and dominated Keshiri society on Keshtah Minor, one of the two major continents on Kesh. At the exposition, Adari was being persecuted by her community for teaching that the landmasses of her homeworldKesh were created by volcanic eruptions. This contradicted the Neshtovar's teachings that Kesh's landmass was created as a result of a battle between two divine groups known as the Skyborn and the Otherside. This persecution took the form of citizens regularly pelting stones at her house and verbally abusing her and her family. Even Adari's mother Eulyn was unsympathetic towards her daughter for challenging the status quo and feared for the lives of Adari's two sons Tona and Finn.

Adari was subsequently summoned by the Neshtovari leader Izri Dazh for a public trial at the Circle Eternal, a large plaza in the heart of Tahv. During the trial, Adari passionately defended her work despite of the hostile atmosphere. Izri also frequently hectored the geologist and accused her of serving the Otherside. While arguing with Izri, the trial was interrupted by a massive explosion which rocked the Cetajan Mountains. Like most in attendance, Adari fled to her home at first but it was soon surrounded by angry Neshtovar who had decided that her "heresy" had brought the anger of the Skyborn upon them. She sent Eulyn and her children to stay at her uncle's house. Adari was subsequently pursued by the enraged townsfolk but managed to escape by riding her uvak Nink to the Cetajan Mountains.

Adari intended to investigate the cause of the explosion. After two days of traveling, Adari and Nink reached the Cetajan Mountains and rested in a mountainside roost. Adari flew Nink towards the source of the explosion. Instead of a volcanic crater, Adari discovered that a large metallic shell, which later turned out to be the SithstarshipOmen, had crashed into the side of a mountain. She also witnessed a man with a red light dropping an object over the side of a precipice. This incident startled Nink and caused Adari to fall off her uvak. However, she was able to grab Nink's foot and held the beast until they reached a seaside perch.

Later that night, Adari discovered a cluster of fires in the mountainside. While she initially feared that the Neshtovar had caught up with her, Adari then received a strange calming message from the mountains and felt compelled to come closer. She then moved towards the fires where she was overpowered and attacked by the "strangers," who turned out to be stranded Sith from the Sith Empire. Before she could be beaten up by the other Sith, she was saved by the man whom she had encountered earlier on the mountains. He introduced himself as Yaru Korsin just as she blacked out. Over the next few days, Adari was nursed back to health by her Sith captors and quickly learned about the identity of the Sith and their starship. Yaru Korsin was the captain of a Sith ship Omen which had crashed on Kesh during the Great Hyperspace War. In return, Adari shared information with her captors about her people, her town of Tahv, and the mythical Skyborn. During this period, Adari also developed a friendship with Yaru Korsin. However, Seelah Korsin, wife of the deceased Devore Korsin, remained suspicious of Adari.

Ultimately, Adari managed to convince Yaru Korsin to allow her to leave with Nink and get help from the Keshiri. After eight days, Adari returned with the Neshtovar and introduced them to the Sith. The Sith were able to awe the Neshtovar with their lightsabers, a technology unknown to the Keshiri, and their ability to levitate objects. Most importantly, they claimed to be the mythical Skyborn, the deities which the Neshtovar revered. As a result, Adari’s status was rapidly elevated from being an ostracized heretic to the esteemed "Daughter of the Skyborn." Adari became the spokesperson of the "Skyborn" who announced that they would reside in Tahv until they could repair their starship and return to the stars. The Skyborn subsequently moved into the homes of the Neshtovar, supplanting the former elite as the new rulers of Keshtah Minor.

Eventually, Adari managed to confront Yaru Korsin about her earlier encounter when she saw him throwing something over the mountainside. She revealed that she had later investigated the object and found that it was a dead man, who had been swept away by the tide. Korsin admitted that the dead man was his estranged brother Devore Korsin but justified his actions by claiming that his brother was a danger to his people. He also reiterated that murder was not abhorred by the Sith. Yaru was also able read Adari’s mind and learnt about her persecution and her deceased husband Zhari. In the end, Korsin persuaded Adari to keep this incident a secret between themselves in return for him teaching her to develop her Force powers. Adari agreed and became a student of Korsin. However, she came to realize that the Sith were not gods despite their Force powers.